7Q9N

Transthyretin complexed with (E)-4-(2-(naphthalen-2-yl)vinyl)benzene-1,2-diol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5298TTR:SB14 complex at 5.2mg/ml in 10mM sodium phosphate pH7.6 and 100mM potassium chloride was mixed 1:1 with 1.3-1.6M sodium citrate and 3.5% glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.2144.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.545α = 90
b = 63.876β = 90
c = 85.137γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2018-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.97993MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4542.5599.90.0550.0570.0160.99919134190820.923
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.471001.5751.6360.4410.77513.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTin-house model1.4538.0939765207399.830.14710.14580.1708RANDOM26.665
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.721.03-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.85
r_dihedral_angle_4_deg13.98
r_dihedral_angle_3_deg11.88
r_rigid_bond_restr9.605
r_dihedral_angle_1_deg6.181
r_angle_other_deg2.526
r_angle_refined_deg1.588
r_chiral_restr0.077
r_bond_other_d0.036
r_gen_planes_other0.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.85
r_dihedral_angle_4_deg13.98
r_dihedral_angle_3_deg11.88
r_rigid_bond_restr9.605
r_dihedral_angle_1_deg6.181
r_angle_other_deg2.526
r_angle_refined_deg1.588
r_chiral_restr0.077
r_bond_other_d0.036
r_gen_planes_other0.016
r_bond_refined_d0.012
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1712
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms40

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction